添加钉钉

codes/run_pipeline.py

@@ -34,6 +34,7 @@ if __name__ == '__main__':
                              "and also run more than one "
                              "node ,like this 'addTarget,addFusion'",
                         default='addQc')
+    parser.add_argument('-d', '--debug', action='store_true', help="debug", default=False)
     args = parser.parse_args()
 
     environ_test()
@@ -48,7 +49,7 @@ if __name__ == '__main__':
     cmd = f'nohup python3 ' \
           f'{run_wdl_path} -n {args.barcode} -s {args.normal} ' \
           f'{"-u " if args.umi else ""} -i {args.input_dir} ' \
-          f'-node {args.start_node} ' \
+          f'-node {args.start_node} {"-d " if args.debug else ""}' \
           f'-o {res_path} -b {args.probe} -p {args.project} -c {args.cancer} -w {args.wdl} ' \
           f'> {res_path}/{args.barcode}_{logname}_run.log ' \
           f'2>> {res_path}/{args.barcode}_{logname}_run.log &'

codes/run_wdl.py

@@ -11,6 +11,9 @@ from datetime import datetime
 import pandas as pd
 import requests
 
+# 创建全局的 Session 对象
+session = requests.Session()
+
 
 def get_branch_nodes(graph, start_node):
     def dfs(node):
@@ -67,14 +70,15 @@ def send_ding(msg):
     '''
     发送钉钉消息功能
     '''
-    url = 'https://oapi.dingtalk.com/robot/send?access_token=d4a0749cc7ff87bd12079a79dd74ca3423becb1ce161c3088acc6628a7a188dd'
+    url = 'https://oapi.dingtalk.com/robot/send?access_token=0c4b2dc1b6a1b459826512cc27adbd14e4f6aa2e661b7a7c284669065bbccfc5'
     data = {"msgtype": "text", "text": {"content": "pipeline:" + str(msg)}, "at": {"isAtAll": True}}
     headers = {'Content-Type': 'application/json;charset=UTF-8'}
     send_data = json.dumps(data).encode('utf-8')
-    ret = requests.post(url=url, data=send_data, headers=headers)
+    session.post(url=url, data=send_data, headers=headers)
+    print(msg)
 
 
-def run(barcode, normal, umi, input_dir, output_dir, project, cancer, probe, wdl, start_node):
+def run(barcode, normal, umi, input_dir, output_dir, project, cancer, probe, wdl, start_node, debug):
     input_dir = os.path.realpath(input_dir)
     output_dir = os.path.realpath(output_dir)
     wdl = os.path.realpath(wdl)
@@ -111,6 +115,8 @@ def run(barcode, normal, umi, input_dir, output_dir, project, cancer, probe, wdl
 
     # 记录开始时间
     start_time = time.time()
+    if not debug:
+        send_ding(msg=f'\n样本: {barcode}\n分析地址: \n{output_dir} \n 开始分析')
     ret = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, encoding="utf-8")
     pidnum = ret.pid
     with open(os.path.join(output_dir, 'pid'), 'w') as pidfile:
@@ -120,8 +126,6 @@ def run(barcode, normal, umi, input_dir, output_dir, project, cancer, probe, wdl
     output, error = ret.communicate()
     print(output, error)
 
-    send_ding(msg=f'样本{barcode}已开始分析，分析地址\n{output_dir}')
-
     stdout = open(os.path.join(output_dir, f'{args.barcode}_{logname}_stdout.log'), 'w')
     stderr = open(os.path.join(output_dir, f'{args.barcode}_{logname}_stderr.log'), 'w')
 
@@ -173,7 +177,8 @@ def run(barcode, normal, umi, input_dir, output_dir, project, cancer, probe, wdl
             stderr.write(file_path + '\n')
             stderr.write(f.read())
             stderr.write('\n\n')
-    send_ding(msg=f'样本{barcode}已分析完成，分析地址\n{output_dir}, 请查看！')
+    if not debug:
+        send_ding(msg=f'\n样本: {barcode}\n分析地址: \n{output_dir} \n 分析完成，请查看！')
     stdout.close()
     stderr.close()
 
@@ -197,7 +202,9 @@ if __name__ == '__main__':
                              "and also run more than one node ,"
                              "like this 'addTarget,addFusion'",
                         default='addQc')
+    parser.add_argument('-d', '--debug', action='store_true', help="debug", default=False)
     args = parser.parse_args()
 
     run(args.barcode, args.normal, args.umi, args.input_dir, args.output_dir,
-        args.project, args.cancer, args.probe, args.wdl, args.start_node)
+        args.project, args.cancer, args.probe, args.wdl, args.start_node, args.debug)
+    session.close()